2021-07-30T08:51:55,348 Created temporary directory: /tmp/pip-ephem-wheel-cache-40xpsp_t 2021-07-30T08:51:55,351 Created temporary directory: /tmp/pip-req-tracker-h49k0zly 2021-07-30T08:51:55,351 Initialized build tracking at /tmp/pip-req-tracker-h49k0zly 2021-07-30T08:51:55,351 Created build tracker: /tmp/pip-req-tracker-h49k0zly 2021-07-30T08:51:55,351 Entered build tracker: /tmp/pip-req-tracker-h49k0zly 2021-07-30T08:51:55,352 Created temporary directory: /tmp/pip-wheel-tncc0cbe 2021-07-30T08:51:55,383 WARNING: The index url "/" seems invalid, please provide a scheme. 2021-07-30T08:51:55,383 WARNING: The index url "t" seems invalid, please provide a scheme. 2021-07-30T08:51:55,384 WARNING: The index url "m" seems invalid, please provide a scheme. 2021-07-30T08:51:55,384 WARNING: The index url "p" seems invalid, please provide a scheme. 2021-07-30T08:51:55,384 Looking in indexes: https://pypi.org/simple, /, t, m, p 2021-07-30T08:51:55,387 WARNING: Location '/elongation-simulators/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-30T08:51:55,387 WARNING: Location 't/elongation-simulators/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-30T08:51:55,387 WARNING: Location 'm/elongation-simulators/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-30T08:51:55,387 WARNING: Location 'p/elongation-simulators/' is ignored: it is either a non-existing path or lacks a specific scheme. 2021-07-30T08:51:55,388 1 location(s) to search for versions of elongation-simulators: 2021-07-30T08:51:55,388 * https://pypi.org/simple/elongation-simulators/ 2021-07-30T08:51:55,388 Fetching project page and analyzing links: https://pypi.org/simple/elongation-simulators/ 2021-07-30T08:51:55,389 Getting page https://pypi.org/simple/elongation-simulators/ 2021-07-30T08:51:55,390 Found index url https://pypi.org/simple 2021-07-30T08:51:55,570 Found link https://files.pythonhosted.org/packages/91/41/df66890ae42dc2e11f26c0ac3e014e648b2c2575df3553bc3430b7c832fc/elongation_simulators-1.0.0.tar.gz#sha256=7fb858683d426c5db11e33f71bafe67ccce54e96bef967a60255fd55963c8e70 (from https://pypi.org/simple/elongation-simulators/), version: 1.0.0 2021-07-30T08:51:55,571 Skipping link: not a file: https://pypi.org/simple/elongation-simulators/ 2021-07-30T08:51:55,588 Given no hashes to check 1 links for project 'elongation-simulators': discarding no candidates 2021-07-30T08:51:55,606 Collecting elongation-simulators==1.0.0 2021-07-30T08:51:55,608 Created temporary directory: /tmp/pip-unpack-_990m_3t 2021-07-30T08:51:57,370 Downloading elongation_simulators-1.0.0.tar.gz (15.6 MB) 2021-07-30T08:52:02,196 Added elongation-simulators==1.0.0 from https://files.pythonhosted.org/packages/91/41/df66890ae42dc2e11f26c0ac3e014e648b2c2575df3553bc3430b7c832fc/elongation_simulators-1.0.0.tar.gz#sha256=7fb858683d426c5db11e33f71bafe67ccce54e96bef967a60255fd55963c8e70 to build tracker '/tmp/pip-req-tracker-h49k0zly' 2021-07-30T08:52:02,197 Running setup.py (path:/tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/setup.py) egg_info for package elongation-simulators 2021-07-30T08:52:02,198 Created temporary directory: /tmp/pip-pip-egg-info-qxuyosix 2021-07-30T08:52:02,198 Running command python setup.py egg_info 2021-07-30T08:52:03,136 running egg_info 2021-07-30T08:52:03,139 creating /tmp/pip-pip-egg-info-qxuyosix/elongation_simulators.egg-info 2021-07-30T08:52:03,139 writing /tmp/pip-pip-egg-info-qxuyosix/elongation_simulators.egg-info/PKG-INFO 2021-07-30T08:52:03,142 writing dependency_links to /tmp/pip-pip-egg-info-qxuyosix/elongation_simulators.egg-info/dependency_links.txt 2021-07-30T08:52:03,144 writing top-level names to /tmp/pip-pip-egg-info-qxuyosix/elongation_simulators.egg-info/top_level.txt 2021-07-30T08:52:03,146 writing manifest file '/tmp/pip-pip-egg-info-qxuyosix/elongation_simulators.egg-info/SOURCES.txt' 2021-07-30T08:52:03,298 reading manifest file '/tmp/pip-pip-egg-info-qxuyosix/elongation_simulators.egg-info/SOURCES.txt' 2021-07-30T08:52:03,299 reading manifest template 'MANIFEST.in' 2021-07-30T08:52:03,300 warning: no previously-included files found matching '.gitmodules' 2021-07-30T08:52:03,301 warning: no previously-included files found matching '.travis.yml' 2021-07-30T08:52:03,301 warning: no previously-included files found matching '.appveyor.yml' 2021-07-30T08:52:03,301 warning: no previously-included files found matching 'Unit-Tests' 2021-07-30T08:52:03,306 warning: no files found matching 'docs' 2021-07-30T08:52:03,374 adding license file 'LICENSE' 2021-07-30T08:52:03,397 writing manifest file '/tmp/pip-pip-egg-info-qxuyosix/elongation_simulators.egg-info/SOURCES.txt' 2021-07-30T08:52:03,469 Source in /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0 has version 1.0.0, which satisfies requirement elongation-simulators==1.0.0 from https://files.pythonhosted.org/packages/91/41/df66890ae42dc2e11f26c0ac3e014e648b2c2575df3553bc3430b7c832fc/elongation_simulators-1.0.0.tar.gz#sha256=7fb858683d426c5db11e33f71bafe67ccce54e96bef967a60255fd55963c8e70 2021-07-30T08:52:03,470 Removed elongation-simulators==1.0.0 from https://files.pythonhosted.org/packages/91/41/df66890ae42dc2e11f26c0ac3e014e648b2c2575df3553bc3430b7c832fc/elongation_simulators-1.0.0.tar.gz#sha256=7fb858683d426c5db11e33f71bafe67ccce54e96bef967a60255fd55963c8e70 from build tracker '/tmp/pip-req-tracker-h49k0zly' 2021-07-30T08:52:03,474 Created temporary directory: /tmp/pip-unpack-tt9dekrw 2021-07-30T08:52:03,475 Building wheels for collected packages: elongation-simulators 2021-07-30T08:52:03,479 Created temporary directory: /tmp/pip-wheel-2ehy3pd3 2021-07-30T08:52:03,479 Building wheel for elongation-simulators (setup.py): started 2021-07-30T08:52:03,479 Destination directory: /tmp/pip-wheel-2ehy3pd3 2021-07-30T08:52:03,480 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-2ehy3pd3 2021-07-30T08:52:04,417 running bdist_wheel 2021-07-30T08:52:04,421 running build 2021-07-30T08:52:04,421 running build_py 2021-07-30T08:52:04,560 creating build 2021-07-30T08:52:04,560 creating build/lib.linux-armv7l-3.9 2021-07-30T08:52:04,561 creating build/lib.linux-armv7l-3.9/concentrations 2021-07-30T08:52:04,562 copying concentrations/__init__.py -> build/lib.linux-armv7l-3.9/concentrations 2021-07-30T08:52:04,564 creating build/lib.linux-armv7l-3.9/elongation 2021-07-30T08:52:04,565 copying elongation/simulationbuilder.py -> build/lib.linux-armv7l-3.9/elongation 2021-07-30T08:52:04,568 copying elongation/__init__.py -> build/lib.linux-armv7l-3.9/elongation 2021-07-30T08:52:04,569 running egg_info 2021-07-30T08:52:04,583 writing elongation_simulators.egg-info/PKG-INFO 2021-07-30T08:52:04,585 writing dependency_links to elongation_simulators.egg-info/dependency_links.txt 2021-07-30T08:52:04,587 writing top-level names to elongation_simulators.egg-info/top_level.txt 2021-07-30T08:52:04,594 reading manifest file 'elongation_simulators.egg-info/SOURCES.txt' 2021-07-30T08:52:04,617 reading manifest template 'MANIFEST.in' 2021-07-30T08:52:04,620 warning: no previously-included files found matching '.gitmodules' 2021-07-30T08:52:04,621 warning: no previously-included files found matching '.travis.yml' 2021-07-30T08:52:04,622 warning: no previously-included files found matching '.appveyor.yml' 2021-07-30T08:52:04,622 warning: no previously-included files found matching 'Unit-Tests' 2021-07-30T08:52:04,628 warning: no files found matching 'docs' 2021-07-30T08:52:04,674 adding license file 'LICENSE' 2021-07-30T08:52:04,708 writing manifest file 'elongation_simulators.egg-info/SOURCES.txt' 2021-07-30T08:52:04,734 copying concentrations/Saccharomyces_cerevisiae.csv -> build/lib.linux-armv7l-3.9/concentrations 2021-07-30T08:52:04,737 running build_ext 2021-07-30T08:52:04,805 cmake version 3.18.4 2021-07-30T08:52:04,805 CMake suite maintained and supported by Kitware (kitware.com/cmake). 2021-07-30T08:52:05,259 -- The CXX compiler identification is GNU 10.2.1 2021-07-30T08:52:05,362 -- Detecting CXX compiler ABI info 2021-07-30T08:52:05,819 -- Detecting CXX compiler ABI info - done 2021-07-30T08:52:05,882 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2021-07-30T08:52:05,884 -- Detecting CXX compile features 2021-07-30T08:52:05,887 -- Detecting CXX compile features - done 2021-07-30T08:52:05,977 -- Found PythonInterp: /usr/bin/python3.9 (found version "3.9.2") 2021-07-30T08:52:06,093 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2021-07-30T08:52:06,112 -- Performing Test HAS_CPP14_FLAG 2021-07-30T08:52:06,562 -- Performing Test HAS_CPP14_FLAG - Success 2021-07-30T08:52:06,584 -- pybind11 v2.5.0 2021-07-30T08:52:06,606 -- Configuring done 2021-07-30T08:52:06,629 -- Generating done 2021-07-30T08:52:06,639 -- Build files have been written to: /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11 2021-07-30T08:52:06,813 ---------- Running CMake prepare ---------------------------------------- 2021-07-30T08:52:07,169 -- The C compiler identification is GNU 10.2.1 2021-07-30T08:52:07,524 -- The CXX compiler identification is GNU 10.2.1 2021-07-30T08:52:07,575 -- Detecting C compiler ABI info 2021-07-30T08:52:07,985 -- Detecting C compiler ABI info - done 2021-07-30T08:52:08,048 -- Check for working C compiler: /usr/bin/cc - skipped 2021-07-30T08:52:08,049 -- Detecting C compile features 2021-07-30T08:52:08,051 -- Detecting C compile features - done 2021-07-30T08:52:08,075 -- Detecting CXX compiler ABI info 2021-07-30T08:52:08,522 -- Detecting CXX compiler ABI info - done 2021-07-30T08:52:08,590 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2021-07-30T08:52:08,591 -- Detecting CXX compile features 2021-07-30T08:52:08,594 -- Detecting CXX compile features - done 2021-07-30T08:52:08,696 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so (found version "3.9.2") 2021-07-30T08:52:08,767 -- Found PythonInterp: /usr/bin/python3 (found version "3.9.2") 2021-07-30T08:52:08,879 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2021-07-30T08:52:08,900 -- Performing Test HAS_CPP14_FLAG 2021-07-30T08:52:09,359 -- Performing Test HAS_CPP14_FLAG - Success 2021-07-30T08:52:09,384 -- pybind11 v2.5.0 2021-07-30T08:52:09,387 -- Configuring done 2021-07-30T08:52:09,573 -- Generating done 2021-07-30T08:52:09,589 CMake Warning: 2021-07-30T08:52:09,590 Manually-specified variables were not used by the project: 2021-07-30T08:52:09,590 pybind11_DIR 2021-07-30T08:52:09,595 -- Build files have been written to: /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0 2021-07-30T08:52:09,607 ---------- Building extensions ---------------------------------------- 2021-07-30T08:52:10,258 Scanning dependencies of target ribosomesimulator 2021-07-30T08:52:10,323 [ 33%] Building CXX object CMakeFiles/ribosomesimulator.dir/concentrationsreader.cpp.o 2021-07-30T08:52:10,332 [ 66%] Building CXX object CMakeFiles/ribosomesimulator.dir/ribosomesimulator.cpp.o 2021-07-30T08:52:15,031 In file included from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:16, 2021-07-30T08:52:15,031 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:52:15,032 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:52:15,032 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/ribosomesimulator.cpp:14: 2021-07-30T08:52:15,032 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h: In function ‘pybind11::detail::internals& pybind11::detail::get_internals()’: 2021-07-30T08:52:15,032 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h:276:28: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations] 2021-07-30T08:52:15,032 276 | PyEval_InitThreads(); 2021-07-30T08:52:15,032 | ^ 2021-07-30T08:52:15,033 In file included from /usr/include/python3.9/Python.h:145, 2021-07-30T08:52:15,033 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/common.h:112, 2021-07-30T08:52:15,033 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pytypes.h:12, 2021-07-30T08:52:15,033 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:13, 2021-07-30T08:52:15,033 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:52:15,034 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:52:15,034 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/ribosomesimulator.cpp:14: 2021-07-30T08:52:15,034 /usr/include/python3.9/ceval.h:130:37: note: declared here 2021-07-30T08:52:15,034 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); 2021-07-30T08:52:15,034 | ^~~~~~~~~~~~~~~~~~ 2021-07-30T08:52:26,321 [100%] Linking CXX shared module build/temp.linux-armv7l-3.9/ribosomesimulator.cpython-39-arm-linux-gnueabihf.so 2021-07-30T08:52:47,846 [100%] Built target ribosomesimulator 2021-07-30T08:52:48,364 Scanning dependencies of target translation 2021-07-30T08:52:48,441 [ 20%] Building CXX object CMakeFiles/translation.dir/elongation_simulation_manager.cpp.o 2021-07-30T08:52:48,442 [ 20%] Building CXX object CMakeFiles/translation.dir/elongation_simulation_processor.cpp.o 2021-07-30T08:52:48,446 [ 30%] Building CXX object CMakeFiles/translation.dir/mrna_reader.cpp.o 2021-07-30T08:52:48,458 [ 40%] Building CXX object CMakeFiles/translation.dir/translation.cpp.o 2021-07-30T08:52:52,419 In file included from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:16, 2021-07-30T08:52:52,420 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:52:52,420 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:52:52,421 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/elongation_simulation_processor.cpp:7: 2021-07-30T08:52:52,421 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h: In function ‘pybind11::detail::internals& pybind11::detail::get_internals()’: 2021-07-30T08:52:52,421 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h:276:28: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations] 2021-07-30T08:52:52,422 276 | PyEval_InitThreads(); 2021-07-30T08:52:52,422 | ^ 2021-07-30T08:52:52,423 In file included from /usr/include/python3.9/Python.h:145, 2021-07-30T08:52:52,424 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/common.h:112, 2021-07-30T08:52:52,424 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pytypes.h:12, 2021-07-30T08:52:52,424 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:13, 2021-07-30T08:52:52,425 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:52:52,425 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:52:52,425 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/elongation_simulation_processor.cpp:7: 2021-07-30T08:52:52,425 /usr/include/python3.9/ceval.h:130:37: note: declared here 2021-07-30T08:52:52,426 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); 2021-07-30T08:52:52,426 | ^~~~~~~~~~~~~~~~~~ 2021-07-30T08:52:53,105 In file included from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:16, 2021-07-30T08:52:53,105 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:52:53,105 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:52:53,106 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/translation.cpp:20: 2021-07-30T08:52:53,106 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h: In function ‘pybind11::detail::internals& pybind11::detail::get_internals()’: 2021-07-30T08:52:53,106 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h:276:28: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations] 2021-07-30T08:52:53,107 276 | PyEval_InitThreads(); 2021-07-30T08:52:53,107 | ^ 2021-07-30T08:52:53,107 In file included from /usr/include/python3.9/Python.h:145, 2021-07-30T08:52:53,108 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/common.h:112, 2021-07-30T08:52:53,108 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pytypes.h:12, 2021-07-30T08:52:53,108 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:13, 2021-07-30T08:52:53,109 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:52:53,109 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:52:53,109 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/translation.cpp:20: 2021-07-30T08:52:53,110 /usr/include/python3.9/ceval.h:130:37: note: declared here 2021-07-30T08:52:53,110 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); 2021-07-30T08:52:53,110 | ^~~~~~~~~~~~~~~~~~ 2021-07-30T08:52:53,911 In file included from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:16, 2021-07-30T08:52:53,912 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:52:53,912 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:52:53,913 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/elongation_simulation_manager.cpp:11: 2021-07-30T08:52:53,913 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h: In function ‘pybind11::detail::internals& pybind11::detail::get_internals()’: 2021-07-30T08:52:53,913 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h:276:28: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations] 2021-07-30T08:52:53,914 276 | PyEval_InitThreads(); 2021-07-30T08:52:53,914 | ^ 2021-07-30T08:52:53,914 In file included from /usr/include/python3.9/Python.h:145, 2021-07-30T08:52:53,915 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/common.h:112, 2021-07-30T08:52:53,915 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pytypes.h:12, 2021-07-30T08:52:53,915 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:13, 2021-07-30T08:52:53,916 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:52:53,916 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:52:53,916 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/elongation_simulation_manager.cpp:11: 2021-07-30T08:52:53,917 /usr/include/python3.9/ceval.h:130:37: note: declared here 2021-07-30T08:52:53,917 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); 2021-07-30T08:52:53,917 | ^~~~~~~~~~~~~~~~~~ 2021-07-30T08:52:59,320 [ 50%] Building CXX object CMakeFiles/translation.dir/initiationterminationcodon.cpp.o 2021-07-30T08:53:01,876 [ 60%] Building CXX object CMakeFiles/translation.dir/concentrationsreader.cpp.o 2021-07-30T08:53:04,137 [ 70%] Building CXX object CMakeFiles/translation.dir/ribosomesimulator.cpp.o 2021-07-30T08:53:04,992 [ 80%] Building CXX object CMakeFiles/translation.dir/mrnaelement.cpp.o 2021-07-30T08:53:07,216 [ 90%] Building CXX object CMakeFiles/translation.dir/elongation_codon.cpp.o 2021-07-30T08:53:10,700 In file included from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:16, 2021-07-30T08:53:10,701 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:53:10,701 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:53:10,701 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/ribosomesimulator.cpp:14: 2021-07-30T08:53:10,701 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h: In function ‘pybind11::detail::internals& pybind11::detail::get_internals()’: 2021-07-30T08:53:10,701 /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/internals.h:276:28: warning: ‘void PyEval_InitThreads()’ is deprecated [-Wdeprecated-declarations] 2021-07-30T08:53:10,701 276 | PyEval_InitThreads(); 2021-07-30T08:53:10,701 | ^ 2021-07-30T08:53:10,702 In file included from /usr/include/python3.9/Python.h:145, 2021-07-30T08:53:10,702 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/detail/common.h:112, 2021-07-30T08:53:10,703 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pytypes.h:12, 2021-07-30T08:53:10,703 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/cast.h:13, 2021-07-30T08:53:10,703 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/attr.h:13, 2021-07-30T08:53:10,703 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/pybind11/include/pybind11/pybind11.h:44, 2021-07-30T08:53:10,703 from /tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/ribosomesimulator.cpp:14: 2021-07-30T08:53:10,703 /usr/include/python3.9/ceval.h:130:37: note: declared here 2021-07-30T08:53:10,703 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); 2021-07-30T08:53:10,703 | ^~~~~~~~~~~~~~~~~~ 2021-07-30T08:53:22,383 [100%] Linking CXX shared module build/temp.linux-armv7l-3.9/translation.cpython-39-arm-linux-gnueabihf.so 2021-07-30T08:53:22,544 /usr/bin/ld: cannot find -ljsoncpp 2021-07-30T08:53:22,612 collect2: error: ld returned 1 exit status 2021-07-30T08:53:22,618 gmake[3]: *** [CMakeFiles/translation.dir/build.make:224: build/temp.linux-armv7l-3.9/translation.cpython-39-arm-linux-gnueabihf.so] Error 1 2021-07-30T08:53:22,619 gmake[2]: *** [CMakeFiles/Makefile2:125: CMakeFiles/translation.dir/all] Error 2 2021-07-30T08:53:22,620 gmake[1]: *** [CMakeFiles/Makefile2:132: CMakeFiles/translation.dir/rule] Error 2 2021-07-30T08:53:22,620 gmake: *** [Makefile:137: translation] Error 2 2021-07-30T08:53:22,626 Traceback (most recent call last): 2021-07-30T08:53:22,626 File "", line 1, in 2021-07-30T08:53:22,628 File "/tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/setup.py", line 101, in 2021-07-30T08:53:22,629 setup( 2021-07-30T08:53:22,629 File "/usr/local/lib/python3.9/dist-packages/setuptools/__init__.py", line 153, in setup 2021-07-30T08:53:22,630 return distutils.core.setup(**attrs) 2021-07-30T08:53:22,630 File "/usr/lib/python3.9/distutils/core.py", line 148, in setup 2021-07-30T08:53:22,630 dist.run_commands() 2021-07-30T08:53:22,631 File "/usr/lib/python3.9/distutils/dist.py", line 966, in run_commands 2021-07-30T08:53:22,631 self.run_command(cmd) 2021-07-30T08:53:22,632 File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command 2021-07-30T08:53:22,633 cmd_obj.run() 2021-07-30T08:53:22,633 File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 223, in run 2021-07-30T08:53:22,634 self.run_command('build') 2021-07-30T08:53:22,634 File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command 2021-07-30T08:53:22,634 self.distribution.run_command(command) 2021-07-30T08:53:22,635 File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command 2021-07-30T08:53:22,636 cmd_obj.run() 2021-07-30T08:53:22,636 File "/usr/lib/python3.9/distutils/command/build.py", line 135, in run 2021-07-30T08:53:22,637 self.run_command(cmd_name) 2021-07-30T08:53:22,637 File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command 2021-07-30T08:53:22,638 self.distribution.run_command(command) 2021-07-30T08:53:22,638 File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command 2021-07-30T08:53:22,639 cmd_obj.run() 2021-07-30T08:53:22,640 File "/tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/setup.py", line 73, in run 2021-07-30T08:53:22,640 subprocess.check_call(cmake_cmd, 2021-07-30T08:53:22,640 File "/usr/lib/python3.9/subprocess.py", line 373, in check_call 2021-07-30T08:53:22,641 raise CalledProcessError(retcode, cmd) 2021-07-30T08:53:22,641 subprocess.CalledProcessError: Command '['cmake', '--build', '../../', '--config', 'Release', '--', 'ribosomesimulator', 'translation', '-j4']' returned non-zero exit status 2. 2021-07-30T08:53:22,728 Building wheel for elongation-simulators (setup.py): finished with status 'error' 2021-07-30T08:53:22,728 ERROR: Failed building wheel for elongation-simulators 2021-07-30T08:53:22,729 Running setup.py clean for elongation-simulators 2021-07-30T08:53:22,729 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-tncc0cbe/elongation-simulators_7f2407c1e3f942e199d6840f042fc0c0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2021-07-30T08:53:23,715 running clean 2021-07-30T08:53:23,717 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-30T08:53:23,720 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-30T08:53:23,723 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-30T08:53:23,724 'build/scripts-3.9' does not exist -- can't clean it 2021-07-30T08:53:23,724 removing 'build' 2021-07-30T08:53:23,789 Failed to build elongation-simulators 2021-07-30T08:53:23,790 ERROR: Failed to build one or more wheels 2021-07-30T08:53:23,791 Exception information: 2021-07-30T08:53:23,791 Traceback (most recent call last): 2021-07-30T08:53:23,791 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-30T08:53:23,791 status = self.run(options, args) 2021-07-30T08:53:23,791 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-30T08:53:23,791 return func(self, options, args) 2021-07-30T08:53:23,791 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-30T08:53:23,791 raise CommandError( 2021-07-30T08:53:23,791 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-30T08:53:23,795 Removed build tracker: '/tmp/pip-req-tracker-h49k0zly'